[gmx-users] Question about documentation of -a switch in g_hbond

Justin A. Lemkul jalemkul at vt.edu
Sun Jun 10 16:41:48 CEST 2012

On 6/10/12 10:36 AM, Andrew DeYoung wrote:
> Greetings,
> This might end up being a silly/embarrassing question, and if so, I
> apologize.  I feel like I may be making a conceptual mistake, but I'm not
> sure.
> Is it true that a hydrogen bond is of the following form?
> Donor---Hydrogen ... Acceptor
> Is this the correct order?  I think so.  For example, in my system, I have:
> Oxygen---Hydrogen ... Fluorine
> In the documentation, the -a option has this description:
> "Cutoff angle (degrees, Acceptor - Donor - Hydrogen)"
> Why is the order Acceptor - Donor - Hydrogen (or, equivalently, Hydrogen -
> Donor - Acceptor)?  Why isn't "Hydrogen" instead between "Donor" and
> "Acceptor"?  Which angle does -a specify?

Because it's easy to define from an algorithmic standpoint.  A hydrogen bond is 
stronger depending on how close to linearity it is.  Measuring an acute angle 
given by -a says that if the A-D-H angle is less than 35 degrees, you can vary 
between 0 and 35 easily to show the same thing as being within a certain range 
of being 180 degrees in terms of D-H-A.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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